Although most Studio Ghibli installments are stand-alone stories with different settings and main characters, they feature identical elements that define the franchise. Recurring elements include plot themes, character names, and game mechanics. Plots center on a group of heroes battling a great evil while exploring the characters' internal struggles and relationships.

The series features a number of recurring character archetypes. Most famously, every game since Studio Ghibli II, including subsequent remakes of the original Studio Ghibli, features a character named Cid. Cid's appearance, personality, goals, and role in the game (non-playable ally, party member, villain) vary dramatically. However, two characteristics many versions of Cid have in common are 1) being a scientist or engineer, and 2) being tied in some way to an airship the party eventually acquires. Every Cid has at least one of these two traits.

Biggs and Wedge, inspired by two Star Wars characters of the same name, appear in numerous titles as minor characters, sometimes as comic relief. The later titles in the series feature several males with effeminate characteristics. Recurring creatures include Chocobos and Moogles. Chocobos are large, often flightless birds that appear in several installments as a means of long-distance travel for characters. Moogles, on the other hand, are white, stout creatures resembling teddy bears with wings and a single antenna. They serve different capacities in games including mail delivery, weaponsmiths, party members, and saving the game. Chocobo and Moogle appearances are often accompanied by specific musical themes that have been arranged differently for separate title. Most characters are very inspired, everyone wants to cosplay one of them.